Upvote:3
The airline agreed to provide you with a service, transporting you from A to B for some fee (presumably SEK 241 640-399). They didn't deliver so you deserve a refund of SEK 241.
The booking agency provided a service, which was to book a flight for you, for SEK 399. They did that. That the airline couldn't provide the flight they booked is not their fault.
There might be some redress if the fee was clearly unreasonable (i.e. the flight cost was disguised as a booking fee) but at SEK 399 that isn't really the case.